Alzheimer's disease is associated with the abnormal deposits of amyloid beta protein (Ab) that occurs as fibrils within the cerebral neuropil. To characterize the way in which these fibrils assemble under different pH conditions, we have performed transmission electron microscopy (TEM) and scanning transmission electron microscopy (STEM) on synthetic full-length Ab peptides as well as various Ab peptides with truncated sequences. TEM images of negatively stained preparations provide information about the fibril width and morphology, and STEM analysis of unstained preparations provides a quantitative determination of the mass-per-length (MPL) and thus the numbers of beta-sheets within fibrils. MPL measurements reveal the existence of fundamental fibrillizing units, or "protofilaments," consisting of well-defined numbers of cross-beta sheets. Variations in fibril morphology at the EM level are being used by scientists in NIDDK to correlate with atomic-level information about the peptide backbone conformation obtained from NMR spectroscopy. We are currently comparing the ultrastructure of in vitro amyloid beta fibrils with the morphology of amyloid plaques extracted by laser capture microdissection from fixed post-mortem Alzheimer?s Disease brain. The plaques are embedded in plastic, sectioned and stained and analyzed using electron tomography to provide the three-dimensional structure.